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[possible-bug] GATK 3.4-46 CombineGVCFs is wrongly assigning * at -1 position of some intervals
We found that whenever the previous interval ends in a deletion, GATK is extending upstream 1 base the following interval and wrongly adds the
* call to it. In most cases this will be a non-issue as you will filter downstream analysis with the same interval files and these lines won't be included. Still it looks like a bug the team might want to look into.
Also we are running CombineGVCFs in "BP_RESOLUTION" mode. Not sure if this makes a difference.
A couple of examples:
#CHROM POS ID REF ALT QUAL FILTER INFO 1 100330153 . C <NON_REF> . . . 1 100330154 . T <NON_REF> . . . 1 100330155 . TC T,<NON_REF> . . BaseQRankSum=-0.572;ClippingRankSum=0;DP=14876;MQ=60;MQRankSum=-1.067;ReadPosRankSum=0.572 1 100335944 . T *,<NON_REF> . . DP=8 1 100335945 . T <NON_REF> . . . 1 100335946 . T <NON_REF> . . . #CHROM POS ID REF ALT QUAL FILTER INFO 1 215916683 . AAGAG A,AAG 9405.15 . AC=4,81;AF=0.008547,0.173;AN=468;BaseQRankSum=-0.061;ClippingRankSum=0.1;DP=25502;FS=0;InbreedingCoeff=-0.2174;MLEAC=2,80;MLEAF=0.004274,0.171;MQ=60;MQRankSum=0.092;QD=1.25;ReadPosRankSum=-1.035;SOR=0.65 1 215916684 . A *,<NON_REF> . . DP=25594 1 215916685 . G *,<NON_REF> . . DP=25593 1 215916686 . A *,<NON_REF> . . DP=25128 1 215916687 . G *,<NON_REF> . . DP=25115 1 215931925 . T *,<NON_REF> . . DP=65 1 215931926 . T <NON_REF> . . . 1 215931927 . T <NON_REF> . . .
Relevant lines in the interval file:
1 100329930 100330155 AGL 0 + 1 100335944 100336147 AGL 0 + 1 215916507 215916687 USH2A 0 - 1 215931925 215932104 USH2A 0 -